Advancing alternatives analysis: The role of predictive toxicology in selecting safer chemical products and processes

Alternatives assessment: An analysis on progress and future needs for research and practice

Alternatives assessment is a science-policy approach to support the informed substitution of chemicals of concern in consumer products and industries, with the intent of avoiding regrettable substitution and facilitating the transition to safer, more sustainable chemicals and products. The field of alternatives assessment has grown steadily in recent decades, particularly after the publication of specific frameworks and the inclusion of substitution and alternatives assessment requirements in a number of policy contexts. Previously, 14 research and practice needs for the field were outlined across five critical areas: comparative hazard assessment, comparative exposure characterization, lifecycle considerations, decision-making and decision analysis, and professional practice. The aim of the current article is twofold: to highlight methodological advances in the growing field of alternatives assessment based on identified research and practice needs and to propose areas for future developments. We assess advances in the field based on the analysis of a broad literature review that captured 154 sources published from 2013 to 2022. The results indicate that research conducted advanced many of the needs identified, but several remain underaddressed. Although the field has clearly grown and taken root over the past decade, there are still research and practice gaps, most notably on the hazard assessment of mixtures or different forms of chemicals, the integration of lifecycle considerations, and the development of practical approaches to address trade-offs in decision-making. We propose modifications to four of the prior research and practice needs in addition to new needs, including the development of standardized hazard assessment approaches for chemical mixtures as well as better integration of equity and/or justice considerations into assessments. Integr Environ Assess Manag 2024;00:1-18. © 2023 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Towards better prediction of xenobiotic genotoxicity: CometChip technology coupled with a 3D model of HepaRG human liver cells

Toxicology is facing a major change in the way toxicity testing is conducted by moving away from animal experimentation towards animal-free methods. To improve the in vitro genotoxicity assessment of chemical and physical compounds, there is an urgent need to accelerate the development of 3D cell models in high-throughput DNA damage detection platforms. Among the alternative methods, hepatic cell lines are a relevant in vitro model for studying the functions of the liver. 3D HepaRG spheroids show improved hepatocyte differentiation, longevity, and functionality compared with 2D HepaRG cultures and are therefore a relevant model for predicting in vivo responses. Recently, the comet assay was developed on 3D HepaRG cells. However, this approach is still low throughput and does not meet the challenge of evaluating the toxicity and risk to humans of tens of thousands of compounds. In this study, we evaluated the performance of the high-throughput in vitro CometChip assay on 2D and 3D HepaRG cells. HepaRG cells were exposed for 48 h to several compounds (methyl methanesulfonate, etoposide, benzo[a]pyrene, cyclophosphamide, 7,12-dimethylbenz[a]anthracene, 2-acetylaminofluorene, and acrylamide) known to have different genotoxic modes of action. The resulting dose responses were quantified using benchmark dose modelling. DNA damage was observed for all compounds except 2-AAF in 2D HepaRG cells and etoposide in 3D HepaRG cells. Results indicate that the platform is capable of reliably identifying genotoxicants in 3D HepaRG cells, and provide further insights regarding specific responses of 2D and 3D models.

Multi-Strategy Assessment of Different Uses of QSAR under REACH Analysis of Alternatives to Advance Information Transparency

Under the Registration, Evaluation, Authorization, and Restriction of Chemicals (REACH) analysis of alternatives (AoA) process, quantitative structure–activity relationship (QSAR) models play an important role in expanding information gathering and organizing frameworks. Increasingly recognized as an alternative to testing under registration. QSARs have become a relevant tool in bridging data gaps and supporting weight of evidence (WoE) when assessing alternative substances. Additionally, QSARs are growing in importance in integrated testing strategies (ITS). For example, the REACH ITS framework for specific endpoints directs registrants to consider non-testing results, including QSAR predictions, when deciding if further animal testing is needed. Despite the raised profile of QSARs in these frameworks, a gap exists in the evaluation of QSAR use and QSAR documentation under authorization. An assessment of the different uses (e.g., WoE and ITS) in which QSAR predictions play a role in evidence gathering and organizing remains unaddressed for AoA. This study approached the disparity in information for QSAR predictions by conducting a substantive review of 24 AoA through May 2017, which contained higher-tier endpoints under REACH. Understanding the manner in which applicants manage QSAR prediction information in AoA and assessing their potential within ITS will be valuable in promoting regulatory use of QSARs and building out future platforms in the face of rapidly evolving technology while advancing information transparency.

A Modern Genotoxicity Testing Paradigm: Integration of the High-Throughput CometChip® and the TGx-DDI Transcriptomic Biomarker in Human HepaRG™ Cell Cultures

Higher-throughput, mode-of-action-based assays provide a valuable approach to expedite chemical evaluation for human health risk assessment. In this study, we combined the high-throughput alkaline DNA damage-sensing CometChip^® assay with the TGx-DDI transcriptomic biomarker (DDI = DNA damage-inducing) using high-throughput TempO-Seq^®, as an integrated genotoxicity testing approach. We used metabolically competent differentiated human HepaRG™ cell cultures to enable the identification of chemicals that require bioactivation to cause genotoxicity. We studied 12 chemicals (nine DDI, three non-DDI) in increasing concentrations to measure and classify chemicals based on their ability to damage DNA. The CometChip^® classified 10/12 test chemicals correctly, missing a positive DDI call for aflatoxin B1 and propyl gallate. The poor detection of aflatoxin B1 adducts is consistent with the insensitivity of the standard alkaline comet assay to bulky lesions (a shortcoming that can be overcome by trapping repair intermediates). The TGx-DDI biomarker accurately classified 10/12 agents. TGx-DDI correctly identified aflatoxin B1 as DDI, demonstrating efficacy for combined used of these complementary methodologies. Zidovudine, a known DDI chemical, was misclassified as it inhibits transcription, which prevents measurable changes in gene expression. Eugenol, a non-DDI chemical known to render misleading positive results at high concentrations, was classified as DDI at the highest concentration tested. When combined, the CometChip^® assay and the TGx-DDI biomarker were 100% accurate in identifying chemicals that induce DNA damage. Quantitative benchmark concentration (BMC) modeling was applied to evaluate chemical potencies for both assays. The BMCs for the CometChip^® assay and the TGx-DDI biomarker were highly concordant (within 4-fold) and resulted in identical potency rankings. These results demonstrate that these two assays can be integrated for efficient identification and potency ranking of DNA damaging agents in HepaRG™ cell cultures.

Drivers of and Obstacles to the Adoption of Toxicogenomics for Chemical Risk Assessment: Insights from Social Science Perspectives

BACKGROUND

Some 20 y ago, scientific and regulatory communities identified the potential of omics sciences (genomics, transcriptomics, proteomics, metabolomics) to improve chemical risk assessment through development of toxicogenomics. Recognizing that regulators adopt new scientific methods cautiously given accountability to diverse stakeholders, the scope and pace of adoption of toxicogenomics tools and data have nonetheless not met the ambitious, early expectations of omics proponents.

OBJECTIVE

Our objective was, therefore, to inventory, investigate, and derive insights into drivers of and obstacles to adoption of toxicogenomics in chemical risk assessment. By invoking established social science frameworks conceptualizing innovation adoption, we also aimed to develop recommendations for proponents of toxicogenomics and other new approach methodologies (NAMs).

METHODS

We report findings from an analysis of 56 scientific and regulatory publications from 1998 through 2017 that address the adoption of toxicogenomics for chemical risk assessment. From this purposeful sample of toxicogenomics discourse, we identified major categories of drivers of and obstacles to adoption of toxicogenomics tools and data sets. We then mapped these categories onto social science frameworks for conceptualizing innovation adoption to generate actionable insights for proponents of toxicogenomics.

DISCUSSION

We identify the most salient drivers and obstacles. From 1998 through 2017, adoption of toxicogenomics was understood to be helped by drivers such as those we labeled Superior scientific understanding, New applications, and Reduced cost & increased efficiency but hindered by obstacles such as those we labeled Insufficient validation, Complexity of interpretation, and Lack of standardization. Leveraging social science frameworks, we find that arguments for adoption that draw on the most salient drivers, which emphasize superior and novel functionality of omics as rationales, overlook potential adopters' key concerns: simplicity of use and compatibility with existing practices. We also identify two perspectives-innovation-centric and adopter-centric-on omics adoption and explain how overreliance on the former may be undermining efforts to promote toxicogenomics. https://doi.org/10.1289/EHP6500.

QSAR Use in REACH Analyses of Alternatives to Predict Human Health and Environmental Toxicity of Alternative Chemical Substances

In 2006, the European Union (EU) enacted the Registration, Evaluation, Authorization, and Restriction of Chemicals (REACH) to address growing concerns of hazardous chemicals in the EU market. Under REACH, companies seeking authorization to use priority substances identified as substances of very high concern (SVHCs) and included in the authorization list must apply and submit health and environmental effects data in analyses of alternatives (AoAs) to the European Chemicals Agency (ECHA). To assess safer alternatives, especially in AoA hazard assessment cases where vital information could be missing or insufficient, quantitative structure-activity relationship (QSAR) nontesting methods have gained increasing acceptance and importance. This article assesses AoA applicants' use of QSAR sources and documentation while looking for meaningful trends. In this assessment, usage and frequency of QSAR sources were evaluated in 189 analyses of alternatives for 15 physicochemical properties and 19 human health and environmental endpoints to determine the scope of purpose of QSAR use in AoAs. We found that only 24 out of 189 applications cited QSAR sources to rank or evaluate the safety of their alternative substances relative to the REACH Annex XIV chemical. For human health and environmental hazard endpoints, applicants cited the Danish (Q)SAR Database (n = 63) and unidentified QSARs (n = 36) most frequently. While QSARs were not used to eliminate an alternative, 7.9% and 1.4% per maximum opportunity (MOP) of hazard endpoint and physicochemical QSAR predictions reported background information on alternatives using weight of evidence (WoE). In addition, 3.0% per MOP of hazard endpoint QSAR predictions supported the safety of the alternative while 0.7% per MOP of physicochemical QSAR predictions gave mixed support for their alternative's safety. Documentation regarding QSARs was absent in all 24 AoAs that used QSARs. Limited QSAR use and missing documentation may be the result of several factors, including inconsistent regulatory guidance. Integr Environ Assess Manag 2020;16:745-760. © 2020 SETAC.

Flow cytometric micronucleus assay and TGx-DDI transcriptomic biomarker analysis of ten genotoxic and non-genotoxic chemicals in human HepaRG™ cells

Background

Modern testing paradigms seek to apply human-relevant cell culture models and integrate data from multiple test systems to accurately inform potential hazards and modes of action for chemical toxicology. In genetic toxicology, the use of metabolically competent human hepatocyte cell culture models provides clear advantages over other more commonly used cell lines that require the use of external metabolic activation systems, such as rat liver S9. HepaRG™ cells are metabolically competent cells that express Phase I and II metabolic enzymes and differentiate into mature hepatocyte-like cells, making them ideal for toxicity testing. We assessed the performance of the flow cytometry in vitro micronucleus (MN) test and the TGx-DDI transcriptomic biomarker to detect DNA damage-inducing (DDI) chemicals in human HepaRG™ cells after a 3-day repeat exposure. The biomarker, developed for use in human TK6 cells, is a panel of 64 genes that accurately classifies chemicals as DDI or non-DDI. Herein, the TGx-DDI biomarker was analyzed by Ion AmpliSeq whole transcriptome sequencing to assess its classification accuracy using this more modern gene expression technology as a secondary objective.

Methods

HepaRG™ cells were exposed to increasing concentrations of 10 test chemicals (six genotoxic chemicals, including one aneugen, and four non-genotoxic chemicals). Cytotoxicity and genotoxicity were measured using the In Vitro MicroFlow® kit, which was run in parallel with the TGx-DDI biomarker.

Results

A concentration-related decrease in relative survival and a concomitant increase in MN frequency were observed for genotoxic chemicals in HepaRG™ cells. All five DDI and five non-DDI agents were correctly classified (as genotoxic/non-genotoxic and DDI/non-DDI) by pairing the test methods. The aneugenic agent (colchicine) yielded the expected positive result in the MN test and negative (non-DDI) result by TGx-DDI.

Conclusions

This next generation genotoxicity testing strategy is aligned with the paradigm shift occurring in the field of genetic toxicology. It provides mechanistic insight in a human-relevant cell-model, paired with measurement of a conventional endpoint, to inform the potential for adverse health effects. This work provides support for combining these assays in an integrated test strategy for accurate, higher throughput genetic toxicology testing in this metabolically competent human progenitor cell line.

Toward Rigorous Materials Production: New Approach Methodologies Have Extensive Potential to Improve Current Safety Assessment Practices

Advanced material development, including at the nanoscale, comprises costly and complex challenges coupled to ensuring human and environmental safety. Governmental agencies regulating safety have announced interest toward acceptance of safety data generated under the collective term New Approach Methodologies (NAMs), as such technologies/approaches offer marked potential to progress the integration of safety testing measures during innovation from idea to product launch of nanomaterials. Divided in overall eight main categories, searchable databases for grouping and read across purposes, exposure assessment and modeling, in silico modeling of physicochemical structure and hazard data, in vitro high-throughput and high-content screening assays, dose-response assessments and modeling, analyses of biological processes and toxicity pathways, kinetics and dose extrapolation, consideration of relevant exposure levels and biomarker endpoints typify such useful NAMs. Their application generally agrees with articulated stakeholder needs for improvement of safety testing procedures. They further fit for inclusion and add value in nanomaterials risk assessment tools. Overall 37 of 50 evaluated NAMs and tiered workflows applying NAMs are recommended for considering safer-by-design innovation, including guidance to the selection of specific NAMs in the eight categories. An innovation funnel enriched with safety methods is ultimately proposed under the central aim of promoting rigorous nanomaterials innovation.

In silico prediction of toxicity and its applications for chemicals at work

OBJECTIVE AND METHODS

This study reviewed the concept of in silico prediction of chemical toxicity for prevention of occupational cancer and future prospects in workers' health. In this review, a new approach to determine the credibility of in silico predictions with raw data is explored, and the method of determining the confidence level of evaluation based on the credibility of data is discussed. I searched various papers and books related to the in silico prediction of chemical toxicity and carcinogenicity. The intention was to utilize the most recent reports after 2015 regarding in silico prediction.

RESULTS AND CONCLUSION

The application of in silico methods is increasing with the prediction of toxic risks to human and the environment. The various toxic effects of industrial chemicals have triggered the recognition of the importance of using a combination of in silico models in the risk assessments. In silico occupational exposure models, industrial accidents, and occupational cancers are effectively managed and chemicals evaluated. It is important to identify and manage hazardous substances proactively through the rigorous evaluation of chemicals.

A Case study on the utility of predictive toxicology tools in alternatives assessments for hazardous chemicals in children's consumer products

Children's consumer products represent an important exposure source for many toxicants. Chemicals of high concern, as designated by the Washington State Child Safe Product Act include phthalates, Bisphenol A (BPA) and parabens, among others. As regulation and reporting requirements increase, so has demand for safer alternatives. This project examines how predictive toxicology and exposure comparison tools can fill gaps in alternatives assessments for hazardous chemicals found in children's products. Phthalates, parabens, BPA and their alternatives were assessed for endocrine disruption and reproductive toxicity using authoritative lists and US Environmental Protection Agency's (EPA) predictive toxicology and exposure comparison tools. Resources included the European Chemical Agency's Endocrine Disruptor Substances of Concern database, Global Harmonization System and Classification of Labeling Chemicals, Quantitative Structural Activity Relationships from the Toxicity Estimation Software Tool, the Toxicological Prioritization Index (ToxPi) score calculated from the ToxCast Database, and No Observable Adverse Effects Levels (NOAELs)/Highest No Effects Levels (HNEL) from animal studies found in the CompTox Chemistry Dashboard. Exposure was assessed using ExpoCast predictions. Though alternatives were rarely included in authoritative lists, predictive toxicology tools suggested that BPA alternatives may not be safer but paraben and phthalate alternatives may be safer. All four paraben and no bisphenol or phthalate alternatives were listed on EPA's Safer Chemical Ingredients List. Overall, we found that predictive toxicology tools help fill gaps for alternatives assessments when existing classifications are incomplete.

New Toxicology Tools and the Emerging Paradigm Shift in Environmental Health Decision-Making

BACKGROUND

Numerous types of rapid toxicity or exposure assays and platforms are providing information relevant to human hazard and exposure identification. They offer the promise of aiding decision-making in a variety of contexts including the regulatory management of chemicals, evaluation of products and environmental media, and emergency response. There is a need to consider both the scientific validity of the new methods and the values applied to a given decision using this new information to ensure that the new methods are employed in ways that enhance public health and environmental protection. In 2018, a National Academies of Sciences, Engineering, and Medicine (NASEM) workshop examined both the toxicological and societal aspects of this challenge.

OBJECTIVES

Our objectives were to explore the challenges of adopting new data streams into regulatory decision-making and highlight the need to align new methods with the information and confidence needs of the decision contexts in which the data may be applied.

METHODS

We go beyond the NASEM workshop to further explore the requirements of different decision contexts. We also call for the new methods to be applied in a manner consistent with the core values of public health and environmental protection. We use the case examples presented in the NASEM workshop to illustrate a range of decision contexts that have applied or could benefit from these new data streams. Organizers of the NASEM workshop came together to further evaluate the main themes from the workshop and develop a joint assessment of the critical needs for improved use of emerging toxicology tools in decision-making. We have drawn from our own experience and individual decision or research contexts as well as from the case studies and panel discussions from the workshop to inform our assessment.

DISCUSSION

Many of the statutes that regulate chemicals in the environment place a high priority on the protection of public health and the environment. Moving away from the sole reliance on traditional approaches and information sources used in hazard, exposure, and risk assessment, toward the more expansive use of rapidly acquired chemical information via in vitro, in silico, and targeted testing strategies will require careful consideration of the information needed and values considerations associated with a particular decision. In this commentary, we explore the ability and feasibility of using emerging data streams, particularly those that allow for the rapid testing of a large number of chemicals across numerous biological targets, to shift the chemical testing paradigm to one in which potentially harmful chemicals are more rapidly identified, prioritized, and addressed. Such a paradigm shift could ultimately save financial and natural resources while ensuring and preserving the protection of public health. https://doi.org/10.1289/EHP4745.

Advancing alternatives assessment for safer chemical substitution: A research and practice agenda

Alternatives assessment has emerged as a science policy field that supports the evaluation and adoption of safer chemistries in manufacturing processes and consumer products. The recent surge in the development and practice of alternatives assessment has revealed notable methodological challenges. Spurred by this need, we convened an informal community of practice comprising industry experts, academics, and scientists within government and nongovernmental organizations to prioritize a research and practice agenda for the next 5 years that, if implemented, would significantly advance the field of alternatives assessment. With input from over 40 experts, the agenda outlines specific needs to advance methods, tools, and guidance in 5 critical areas: hazard assessment, comparative exposure characterization, life cycle considerations, decision making, and professional practice. Fifteen research and practice needs were identified, ranging from relatively simple efforts to define a minimum hazard data set to the development of more complex performance and decision-analytic methods and data integration tools. Some research needs involve adapting existing approaches to the alternatives assessment context, while others will require the development of entirely new methods and tools. The proposed research and practice agenda is ambitious. Implementing it will require expanding the current network of researchers from academia, government, and industry, as well as increased funding for methodological, application, and evaluation research. Integr Environ Assess Manag 2018;00:000-000. © 2018 SETAC.

Multicriteria Decision Analysis Characterization of Chemical Hazard Assessment Data Sources

Chemical hazard assessment (CHA), which aims to investigate the inherent hazard potential of chemicals, has been developed with the purpose of promoting safer consumer products. Despite the increasing use of CHA in recent years, finding adequate and reliable toxicity data required for CHA is still challenging due to issues regarding data completeness and data quality. Also, collecting data from primary toxicity reports or literature can be time consuming, which promotes the use of secondary data sources instead. In this study, we evaluate and characterize numerous secondary data sources on the basis of 5 performance attributes: reliability, adequacy, transparency, volume, and ease of use. We use GreenScreen for Safer Chemicals v1.4 as the CHA framework, which defines the endpoints of interest used in this analysis. We focused upon 34 data sources that reflect 3 types of secondary data: chemical-oriented data sources, hazard-trait-oriented data sources, and predictive data sources. To integrate and analyze the evaluation results, we applied 2 multicriteria decision analysis (MCDA) methodologies: multiattribute utility theory (MAUT) and stochastic multiobjective acceptability analysis (SMAA). Overall, the findings in this research program allow us to explore the relative importance of performance criteria and the data source quality for effectively conducting CHA. Integr Environ Assess Manag 2019;00:1-14. © 2019 SETAC.

Lessons from the 2018 International Symposium on Alternatives Assessment: Advances and Reflections on Practice and Ongoing Needs to Build the Field

Alternatives assessment is gaining traction as a systematic method to support the informed substitution of chemicals of concern. The 2nd International Symposium on Alternatives Assessment, on 1-2 November 2018, convened nearly 150 professionals from government agencies, industry, consultant firms, academia, and advocacy organizations to advance a greater understanding of the evolving methods, practices, and challenges in the use of alternatives assessment. This article reviews highlights and lessons from the symposium, including 1) notable advances in methods, 2) shared insights from practitioners on best practices as well as inherent tensions and challenges, and 3) research and practice needs in the field that can be addressed by organizations such as the newly launched Association for the Advancement of Alternatives Assessment. Being interdisciplinary in nature, the establishment of educational frameworks across disciplines and inclusion of diverse expertise in hazard and exposure assessments, life cycle impacts considerations, design principles, and economic and engineering evaluations will ensure continued growth of the field. Integr Environ Assess Manag 2019;00:1-8. © 2019 SETAC.

Optimization of a Deep-Learning Method Based on the Classification of Images Generated by Parameterized Deep Snap a Novel Molecular-Image-Input Technique for Quantitative Structure-Activity Relationship (QSAR) Analysis

Numerous chemical compounds are distributed around the world and may affect the homeostasis of the endocrine system by disrupting the normal functions of hormone receptors. Although the risks associated with these compounds have been evaluated by acute toxicity testing in mammalian models, the chronic toxicity of many chemicals remains due to high cost of the compounds and the testing, etc. However, computational approaches may be promising alternatives and reduce these evaluations. Recently, deep learning (DL) has been shown to be promising prediction models with high accuracy for recognition of images, speech, signals, and videos since it greatly benefits from large datasets. Recently, a novel DL-based technique called DeepSnap was developed to conduct QSAR analysis using three-dimensional images of chemical structures. It can be used to predict the potential toxicity of many different chemicals to various receptors without extraction of descriptors. DeepSnap has been shown to have a very high capacity in tests using Tox21 quantitative qHTP datasets. Numerous parameters must be adjusted to use the DeepSnap method but they have not been optimized. In this study, the effects of these parameters on the performance of the DL prediction model were evaluated in terms of the loss in validation as an indicator for evaluating the performance of the DL using the toxicity information in the Tox21 qHTP database. The relations of the parameters of DeepSnap such as (1) number of molecules per SDF split into (2) zoom factor percentage, (3) atom size for van der waals percentage, (4) bond radius, (5) minimum bond distance, and (6) bond tolerance, with the validation loss following quadratic function curves, which suggests that optimal thresholds exist to attain the best performance with these prediction models. Using the parameter values set with the best performance, the prediction model of chemical compounds for CAR agonist was built using 64 images, at 105° angle, with AUC of 0.791. Thus, based on these parameters, the proposed DeepSnap-DL approach will be highly reliable and beneficial to establish models to assess the risk associated with various chemicals.

The Adverse Outcome Pathway: A Multifaceted Framework Supporting 21st Century Toxicology

The adverse outcome pathway (AOP) framework serves as a knowledge assembly, interpretation, and communication tool designed to support the translation of pathway-specific mechanistic data into responses relevant to assessing and managing risks of chemicals to human health and the environment. As such, AOPs facilitate the use of data streams often not employed by risk assessors, including information from in silico models, in vitro assays and short-term in vivo tests with molecular/biochemical endpoints. This translational capability can increase the capacity and efficiency of safety assessments both for single chemicals and chemical mixtures. Our mini-review describes the conceptual basis of the AOP framework and aspects of its current status relative to use by toxicologists and risk assessors, including four illustrative applications of the framework to diverse assessment scenarios.